Research workbench
Yeast mitochondrial processing peptidase beta-E73Q mutant complexed with cytochrome C oxidase IV signal peptide
Analyse Yeast mitochondrial processing peptidase beta-E73Q mutant complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HR8
- Type
- protein
- Length
- 3,598 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mitochondrial processing peptidase alpha subunit; Mitochondrial processing peptidase beta…
- EC
- 3.4.24.64, 1.9.3.1
- UniProt
- P11914, P10507, P04037
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 11 distinct chains · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 452 | 44% helix, 17% strand | P11914 |
| B | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 439 | 46% helix, 20% strand | P10507 |
| C | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 448 | 45% helix, 17% strand | P11914 |
| D, F | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 443 | 45% helix, 20% strand | P10507 |
| E | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 445 | 44% helix, 17% strand | P11914 |
| G | Mitochondrial processing peptidase alpha subunit (EC 3.4.24.64) | protein | 448 | 44% helix, 17% strand | P11914 |
| H | Mitochondrial processing peptidase beta subunit (EC 3.4.24.64) | protein | 441 | 46% helix, 20% strand | P10507 |
| O | Cytochrome C oxidase polypeptide IV (EC 1.9.3.1) | protein | 13 | 0% helix, 23% strand | P04037 |
| P | Cytochrome C oxidase polypeptide IV (EC 1.9.3.1) | protein | 9 | 0% helix, 33% strand | P04037 |
| Q | Cytochrome C oxidase polypeptide IV (EC 1.9.3.1) | protein | 10 | 0% helix, 30% strand | P04037 |
| R | Cytochrome C oxidase polypeptide IV (EC 1.9.3.1) | protein | 7 | 0% helix, 29% strand | P04037 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, D, F, H, R
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · 2 copies · chains A, E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1153 | 0.86 | 0.87 | 135 | EPE |
| 2 | 651 | 0.80 | 0.85 | 40 | empty |
| 3 | 609 | 0.71 | 0.79 | 68 | empty |
| 4 | 748 | 0.71 | 0.77 | 89 | empty |
| 5 | 79 | 0.70 | 0.95 | 23 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1753 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1678 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 1634 Ų buried · 19 hydrogen bonds · protein-protein
- G–H · 1572 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 1299 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 1HR8 · Yeast Mitochondrial Processing Peptidase beta-E73Q Mutant Complexed with Cytochrome C… · the same entry in another collection · chain R against R, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P11914
- Every structure of UniProt P10507
- Every structure of UniProt P04037
- Elsewhere: RCSB PDB 1HR8 · PDBe 1HR8 · UniProt P11914 · UniProt P10507 · UniProt P04037
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